First of all, you are still able to remove towers of players that left the game, you even get the sell coins for doing so which is nice.
On the actual topic of the post, there are definitely plenty of strategies that involve placing 3x3 towers on 5x5 squares (as shown in the video above), mainly because there aren't enough 5x5 towers to start with. There's only 3 different towers and one of them can only be placed once. Plus in the early game, all of these towers are relatively expensive and on maps like Perilous where there isn't much space at the very start, it's better to place something there to handle the zombies and spiders than just leave it empty. Usually this tower can be replaced later on when it's worth buying the more expensive tower anyway at the cost of only 100 coins or so thanks to the 60% sell price. Maybe if there were more towers to place in these squares and the archer tower "bug" gets fixed, this might be able to happen but for now there isn't a good enough reason to fully lock out other towers. Now on the other hand, for placing 5x5's on 3x3s, I can't think of any reason to do this considering that any of the towers right now are not as good as the 4 (or even 6 if placed badly) towers you can place there, even at full upgrades. While a lv3 turret might be better than 4 lv1 archers, it definitely isn't as good as 2 maxed archers a sorceror and a zeus, so maybe 3x3's can at least be locked out of, plus it can fix placing towers incorrectly and trolling with lv1s by placing off center. Of course, only exception would be the 15x8 areas with 5 3x3s and 3 5x5s in which this may work a bit differently. Anyway that's my thoughts, thanks for reading my massive wall of text on this!